Merge pull request #119 from gdrplatform/GDR-2535

Gdr 2535

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: gDRutils
 Type: Package
 Title: A package with helper functions for processing drug response data
-Version: 1.1.17
-Date: 2024-05-22
+Version: 1.3.1
+Date: 2024-05-27
 Authors@R: c(person("Bartosz", "Czech", role=c("aut"),
                    comment = c(ORCID = "0000-0002-9908-3007")),
              person("Arkadiusz", "Gladki", role=c("cre", "aut"), email="[email protected]",

NEWS.md

@@ -1,3 +1,6 @@
+## gDRutils 1.3.1 - 2024-05-27
+* synchronize Bioconductor and GitHub versioning
+
 ## gDRutils 1.1.17 - 2024-05-22
 * fix check notes
 

inst/test_settings.json

@@ -0,0 +1,29 @@
+{
+    "DICT": {
+        "fifty_lower_limit": 0.0001,
+        "fifty_upper_limit": 30,
+        "max_upper_limit": 1.1,
+        "range_lower_limit": -0.1
+    },
+    "DICT_WITH_LOGICAL": {
+        "axisTitleText": true,
+        "titleText": true
+    },
+    "DICT_WITH_LISTS": {
+        "GR AOC within set range": [
+            0,
+            1
+        ],
+        "RV AOC within set range": [
+            0,
+            1
+        ]
+    },
+    "LIST": [
+        "rId",
+        "cId",
+        "r Id",
+        "c Id"
+    ],
+    "STRING": "fixed"
+}

inst/test_settings_2.json

@@ -0,0 +1,129 @@
+{
+    "FILTERED_OUT_COLS_COMBOS": [
+        "rId",
+        "cId",
+        "r Id",
+        "c Id"
+    ],
+    "FIXED_PREFIX": "fixed",
+    "METRIC_WISH_LIST": [
+        "GR50",
+        "IC50",
+        "GR Max",
+        "E Max",
+        "EC50",
+        "GR Mean",
+        "RV Mean",
+        "GR AOC within set range",
+        "RV AOC within set range"
+    ],
+    "METRIC_WISH_LIST_CURVE": [
+        "GR value",
+        "Relative Viability"
+    ],
+    "METRICS_TRANSFORMED": [
+        "GR50",
+        "IC50",
+        "EC50"
+    ],
+    "SUPPORTED_FILE_TYPES_AUTO": [
+        "text/tsv",
+        "text/tab-separated-values",
+        ".csv",
+        ".xlsx",
+        ".tsv"
+    ],
+    "SUPPORTED_FILE_TYPES_MANIFEST": [
+        "text/tsv",
+        "text/tab-separated-values",
+        "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"
+    ],
+    "SUPPORTED_FILE_TYPES_TREATMENT": [
+        "text/tsv",
+        "text/tab-separated-values",
+        "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"
+    ],
+    "SUPPORTED_FILE_TYPES_RAWDATA": [
+        "text/csv",
+        "text/tsv",
+        "text/tab-separated-values",
+        "text/tab-separated-values,text/plain",
+        "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"
+    ],
+    "VIS_COLS_NORM": [
+        "drug_name",
+        "drug_moa",
+        "drug_name2",
+        "drug_moa2",
+        "drug_name3",
+        "drug_moa3",
+        "cellline_name",
+        "cellline_tissue",
+        "cellline_subtype",
+        "UserCellLineDesignation",
+        "GR value",
+        "Relative Viability",
+        "CorrectedReadout",
+        "drug",
+        "drug2",
+        "drug3",
+        "cellline",
+        "cellline_ref_div_time",
+        "concentration",
+        "concentration2",
+        "concentration3"
+    ],
+    "VIS_COLS_AVG": [
+        "drug_name",
+        "drug_moa",
+        "drug_name2",
+        "drug_moa2",
+        "drug_name3",
+        "drug_moa3",
+        "cellline_name",
+        "cellline_tissue",
+        "cellline_subtype",
+        "UserCellLineDesignation",
+        "GR value",
+        "Relative Viability",
+        "Std GR value",
+        "Std Relative Viability",
+        "drug",
+        "drug2",
+        "drug3",
+        "cellline",
+        "cellline_ref_div_time",
+        "concentration",
+        "concentration2",
+        "concentration3"
+    ],
+    "VIS_COLS_METRICS": [
+        "drug_name",
+        "drug_moa",
+        "drug_name2",
+        "drug_moa2",
+        "drug_name3",
+        "drug_moa3",
+        "cellline_name",
+        "cellline_tissue",
+        "cellline_subtype",
+        "UserCellLineDesignation",
+        "Data Source",
+        "GR AOC",
+        "RV AOC",
+        "RV Mean",
+        "GR Mean",
+        "IC50",
+        "GR50",
+        "E Max",
+        "GR Max",
+        "E Inf",
+        "GR Inf",
+        "drug",
+        "drug2",
+        "drug3",
+        "cellline",
+        "cellline_ref_div_time",
+        "Highest log10(conc.)"
+    ]
+}

tests/testthat/test-convert_mae_se_assay_to_dt.R

@@ -200,7 +200,7 @@ test_that("convert_mae_assay_to_dt works as expected", {
 
 
 test_that("convert_se_assay_to_custom_dt works fine", {
-  json_path <- system.file(package = "gDRcomponents", "settings.json")
+  json_path <- system.file(package = "gDRutils", "test_settings_2.json")
   s <- get_settings_from_json(json_path = json_path)
 
   se <- get_synthetic_data("finalMAE_small")[[1]]

tests/testthat/test-json_const.R

@@ -5,7 +5,7 @@ test_that("get_settings_from_json works as expected", {
     "Assertion on 'json_path' failed"
   )
   json_path <-
-    system.file(package = "gDRcomponents", "test_settings.json")
+    system.file(package = "gDRutils", "test_settings.json")
   expect_error(
     get_settings_from_json(s = "no_such_entry", json_path = json_path),
     "Assertion on 's' failed"

tests/testthat/test-utils.R

@@ -468,7 +468,7 @@ test_that("get_additional_variables works as expected", {
 
 
 test_that("convert_se_assay_to_custom_dt works fine", {
-  json_path <- system.file(package = "gDRcomponents", "settings.json")
+  json_path <- system.file(package = "gDRutils", "test_settings_2.json")
   s <- get_settings_from_json(json_path = json_path)
 
   se <- get_synthetic_data("finalMAE_small")[[1]]